Both of these methods use IBD/IBS values to detect sample contamination. Are there any more methods that can be used for quality control of NGS data for sample contamination? Please suggest me all the methods that you are aware of. Thanks!
If you are designing an experiment, I recommend using a unique spike-in sequence per well to detect cross-contamination (BBMap's Seal works well for calculating the cross-contamination rates).
For scenarios where you are multiplexing different organisms together, you can again use Seal for detection/quantification, or use CrossBlock for fully automatic, reference-free cross-contamination detection and removal. It does not work for cross-contamination between same-organism libraries.
If you already have data, and it's all one organism with no spike-ins, it's too late to accurately detect or remove cross-contamination. As your links indicate, there are ways to estimate it, but it's best to design the experiment correctly from the beginning, with spike-ins.